From 1c94033579e1836c0743460cab6c22cf57c498f5 Mon Sep 17 00:00:00 2001 From: epiverse-trace-bot Date: Wed, 16 Jul 2025 23:42:48 +0000 Subject: [PATCH 1/2] Automated release blog post `superspreading` - `v0.4.0` --- .../index/execute-results/html.json | 15 +++++ posts/superspreading_v0.4.0/index.qmd | 57 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 _freeze/posts/superspreading_v0.4.0/index/execute-results/html.json create mode 100644 posts/superspreading_v0.4.0/index.qmd diff --git a/_freeze/posts/superspreading_v0.4.0/index/execute-results/html.json b/_freeze/posts/superspreading_v0.4.0/index/execute-results/html.json new file mode 100644 index 00000000..d5ca125f --- /dev/null +++ b/_freeze/posts/superspreading_v0.4.0/index/execute-results/html.json @@ -0,0 +1,15 @@ +{ + "hash": "72ae3b7079ead8e908a280d082fbbaf2", + "result": { + "engine": "knitr", + "markdown": "---\ntitle: \"superspreading v0.4.0\"\nauthor:\n - name: \"The Epiverse-TRACE development team\"\ndate: \"2025-07-16\"\ncategories: [new-release]\ncode-link: true\n---\n\n\nWe are very excited to announce the release of a new [superspreading](https://epiverse-trace.github.io/superspreading) version v0.4.0.\nHere is an automatically generated summary of the changes in this version.\n\n\n::: {.cell}\n\n```{.r .cell-code}\nlibrary(superspreading)\n```\n:::\n\n\nThe fourth minor release of the _superspreading_ package contains new functionality, a new vignette and various minor improvements to documentation.\n\nWith this release the development status of the package has been updated from _experimental_ to _stable_. \n\n## New features\n\n* The `probability_emergence()` function has been added to calculate the probability that a pathogen introduced to humans can evolve and emerge to cause a sustained human-to-human outbreak, implementing and extending the framework of [Antia et al. (2003)](https://doi.org/10.1038/nature02104) (#124, #133).\n\n* A new vignette, `emergence.Rmd`, has been added that covers the functionality of `probability_emergence()` and reproduces the two figures from [Antia et al. (2003)](https://doi.org/10.1038/nature02104) as well as a figure using the multiple introductions extension (#124, #133).\n\n* Alt-text has been added to all plots across all vignettes (#129).\n\n## Breaking changes\n\n* The `percent_transmission` argument in `proportion_transmission()` has been renamed to `prop_transmission` (#130).\n\n## Minor changes\n\n* An `.aspell/` folder is added to the package including `defaults.R` and `superspreading.rds` to supply a wordlist to the CRAN spell checking to avoid quoting names in the `DESCRIPTION` (#127). \n\n* Package and function documentation has been updated. Vignette changes include minor reworking of text, updating any information or links that were outdated; function documentation is styled more consistently and follows the [Tidyverse style guide](https://style.tidyverse.org/documentation.html) (#131, #134).\n\n* Internal code style has been updated to adhere to current best practice (#125).\n\n* The package lifecycle badge has been updated from _experimental_ to _stable_. CRAN status, CRAN downloads, repo status and Zenodo DOI badges have been added to the `README` (#119, #132).\n\n* The {pkgdown} `development: mode` has been set to `auto` now the package is hosted on CRAN (#118).\n\n## Bug fixes\n\n* None\n\n## Deprecated and defunct\n\n* None\n\n\n## Acknowledgements\n\n[@chartgerink](https://github.com/chartgerink) [@joshwlambert](https://github.com/joshwlambert)\n", + "supporting": [], + "filters": [ + "rmarkdown/pagebreak.lua" + ], + "includes": {}, + "engineDependencies": {}, + "preserve": {}, + "postProcess": true + } +} \ No newline at end of file diff --git a/posts/superspreading_v0.4.0/index.qmd b/posts/superspreading_v0.4.0/index.qmd new file mode 100644 index 00000000..8e1d8fbc --- /dev/null +++ b/posts/superspreading_v0.4.0/index.qmd @@ -0,0 +1,57 @@ +--- +title: "superspreading v0.4.0" +author: + - name: "The Epiverse-TRACE development team" +date: "2025-07-16" +categories: [new-release] +code-link: true +--- + + +We are very excited to announce the release of a new [superspreading](https://epiverse-trace.github.io/superspreading) version v0.4.0. +Here is an automatically generated summary of the changes in this version. + +```{r} +library(superspreading) +``` + +The fourth minor release of the _superspreading_ package contains new functionality, a new vignette and various minor improvements to documentation. + +With this release the development status of the package has been updated from _experimental_ to _stable_. + +## New features + +* The `probability_emergence()` function has been added to calculate the probability that a pathogen introduced to humans can evolve and emerge to cause a sustained human-to-human outbreak, implementing and extending the framework of [Antia et al. (2003)](https://doi.org/10.1038/nature02104) (#124, #133). + +* A new vignette, `emergence.Rmd`, has been added that covers the functionality of `probability_emergence()` and reproduces the two figures from [Antia et al. (2003)](https://doi.org/10.1038/nature02104) as well as a figure using the multiple introductions extension (#124, #133). + +* Alt-text has been added to all plots across all vignettes (#129). + +## Breaking changes + +* The `percent_transmission` argument in `proportion_transmission()` has been renamed to `prop_transmission` (#130). + +## Minor changes + +* An `.aspell/` folder is added to the package including `defaults.R` and `superspreading.rds` to supply a wordlist to the CRAN spell checking to avoid quoting names in the `DESCRIPTION` (#127). + +* Package and function documentation has been updated. Vignette changes include minor reworking of text, updating any information or links that were outdated; function documentation is styled more consistently and follows the [Tidyverse style guide](https://style.tidyverse.org/documentation.html) (#131, #134). + +* Internal code style has been updated to adhere to current best practice (#125). + +* The package lifecycle badge has been updated from _experimental_ to _stable_. CRAN status, CRAN downloads, repo status and Zenodo DOI badges have been added to the `README` (#119, #132). + +* The {pkgdown} `development: mode` has been set to `auto` now the package is hosted on CRAN (#118). + +## Bug fixes + +* None + +## Deprecated and defunct + +* None + + +## Acknowledgements + +[@chartgerink](https://github.com/chartgerink) [@joshwlambert](https://github.com/joshwlambert) From 56751557c9660a710772f6eee91d17b283799663 Mon Sep 17 00:00:00 2001 From: Chris Hartgerink Date: Mon, 21 Jul 2025 13:30:34 +0200 Subject: [PATCH 2/2] Fix lint --- posts/superspreading_v0.4.0/index.qmd | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/posts/superspreading_v0.4.0/index.qmd b/posts/superspreading_v0.4.0/index.qmd index 8e1d8fbc..9185b8c1 100644 --- a/posts/superspreading_v0.4.0/index.qmd +++ b/posts/superspreading_v0.4.0/index.qmd @@ -17,7 +17,7 @@ library(superspreading) The fourth minor release of the _superspreading_ package contains new functionality, a new vignette and various minor improvements to documentation. -With this release the development status of the package has been updated from _experimental_ to _stable_. +With this release the development status of the package has been updated from _experimental_ to _stable_. ## New features @@ -33,7 +33,7 @@ With this release the development status of the package has been updated from _e ## Minor changes -* An `.aspell/` folder is added to the package including `defaults.R` and `superspreading.rds` to supply a wordlist to the CRAN spell checking to avoid quoting names in the `DESCRIPTION` (#127). +* An `.aspell/` folder is added to the package including `defaults.R` and `superspreading.rds` to supply a wordlist to the CRAN spell checking to avoid quoting names in the `DESCRIPTION` (#127). * Package and function documentation has been updated. Vignette changes include minor reworking of text, updating any information or links that were outdated; function documentation is styled more consistently and follows the [Tidyverse style guide](https://style.tidyverse.org/documentation.html) (#131, #134). @@ -51,7 +51,6 @@ With this release the development status of the package has been updated from _e * None - ## Acknowledgements [@chartgerink](https://github.com/chartgerink) [@joshwlambert](https://github.com/joshwlambert)